PROTEOMICS CORE 1. OVERVIEW AND MAIN OBJECTIVES The mission of the Neuroscience Proteomics Facility is to provide identification, characterization, and detailed analysis of proteins, peptides, carbohydrates and drug-like small molecules. This facility will allow access to and thereby foster collaborations among Neuroscientists on the La Jolla Torrey Pines Mesa (comprised primarily of Burnham, Salk, Scripps, and UCSD neuroscientists). The facility will leverage the existing infrastructure and knowledge-base of the Burnham Institute for Medical Research's (BIMR's) existing Proteomics Center as well as state-of-the-art mass spectrometry (MS) at The Scripps Research Institute (TSRI) and The Salk Institute, which constitute Satellite Centers located across the street from BIMR on North Torrey Pines Road in La Jolla (and within half a mile from UCSD). Presently this Core Facility at BIMR is part of the Burnham's NIH-funded Cancer Center with little or no access to neuroscientists on the La Jolla Torrey Pines Mesa. Under the present application for an NIH Blueprint Grant for Neuroscience Center Cores, all modern proteomic technologies will be available to neuroscience users of the Facility including comprehensive proteomic analysis of complex proteomes using Multi-dimensional Protein Identification (MUDPIT), activity-based enzyme profiling with chemical mass tags, Product Terminal Isotope Coding for the identification of substrates for proteases (products of proteolysis), phospho-peptide and protein identification using precursor ion scanning, neutral loss scanning and MS3 scanning, and automated high-throughput MALDI-TOF/TOF analysis of protein and peptide mixtures. The Facility also performs the more routine mass analysis of intact recombinant proteins and synthetic peptides and glycopeptides, protein identification from gel slices/spots using peptide mass fingerprinting and peptide sequencing. In the spring of 2006 the Director of the Facility will also apply for funds to purchase an FTMS which will provide the highest mass accuracy and resolution, broad fragmentation capability (such as CID, ECD and IRMPD) and the ability to perform de novo peptide and protein sequencing (top-down proteomics) and directly characterize the most complex post-translational modifications in intact proteins, without prior digestion and processing of the sample. A primary objective for this award is to integrate the proteomics efforts of the La Jolla Neurobiology community into the existing Proteomics Center at the Burnham Institute for Medical Research. This will involve the purchase of additional instrumentation (an LTQ Ion Trap in Year 1), and the hiring of additional personnel. By amalgamating the neuroscience Proteomics Shared Resource with that of the current Center (which includes the Proteomics Facility for the Burnham's Cancer Center as well as the NTCNP Center on Proteolytic Pathways), we will be able to capitalize on the considerable instrumentation and expertise of the existing Center for the benefit of the Neuroscience community. The current grant application will facilitate equal access to these facilities by Neuroscientists, who do not have access currently because the facility is in the Cancer Center. The integration of the Neuroscience proteomics effort into the existing Proteomics Center will provide a substantial jump-start for the Neuroscience proteomics effort. In addition to the current equipment at the Burnham Institute for Medical Research (BIMR) listed above, which is under the direction of Dr. Jeff Smith, satellite facilities are also available at The Salk Institute (under the direction of Wolfgang Fischer) and at The Scripps Research Institute (TSRI), under the direction of noted proteomics authority John Yates, III.